Marcin Kosinski
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/RTCGA |
| Branch: RELEASE_3_10 |
| Last Commit: 1ec6cf6 |
| Last Changed Date: 2019-10-29 13:09:26 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:28 -0400 (Wed, 15 Apr 2020).
| Package 1489/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTCGA 1.16.0 Marcin Kosinski
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RTCGA |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RTCGA_1.16.0.tar.gz |
| StartedAt: 2020-04-15 06:19:14 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:43:13 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1438.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RTCGA.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RTCGA_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCGA.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCGA/DESCRIPTION' ... OK
* this is package 'RTCGA' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'RTCGA' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:23: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/installTCGA.Rd:16: file link 'install_github' in package 'devtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCGA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
availableDates: no visible binding for global variable '.'
downloadTCGA: no visible binding for global variable '.'
ggbiplot: no visible binding for global variable 'xvar'
ggbiplot: no visible binding for global variable 'yvar'
ggbiplot: no visible global function definition for 'muted'
ggbiplot: no visible binding for global variable 'varname'
ggbiplot: no visible binding for global variable 'angle'
ggbiplot: no visible binding for global variable 'hjust'
read.mutations: no visible binding for global variable '.'
read.rnaseq: no visible binding for global variable '.'
survivalTCGA: no visible binding for global variable 'times'
whichDateToUse: no visible binding for global variable '.'
Undefined global functions or variables:
. angle hjust muted times varname xvar yvar
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expressionsTCGA 302.48 6.90 315.72
heatmapTCGA 194.92 20.10 215.25
boxplotTCGA 175.17 8.15 194.80
kmTCGA 21.22 0.05 21.61
survivalTCGA 17.75 0.00 17.75
mutationsTCGA 10.06 0.00 10.06
theme_RTCGA 9.87 0.00 9.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expressionsTCGA 218.03 0.62 218.71
heatmapTCGA 144.38 0.17 144.54
boxplotTCGA 125.21 0.99 126.33
kmTCGA 13.60 0.02 13.61
survivalTCGA 10.95 0.03 10.98
mutationsTCGA 6.69 0.00 6.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCGA.Rcheck/00check.log'
for details.
RTCGA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/RTCGA_1.16.0.tar.gz && rm -rf RTCGA.buildbin-libdir && mkdir RTCGA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGA.buildbin-libdir RTCGA_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL RTCGA_1.16.0.zip && rm RTCGA_1.16.0.tar.gz RTCGA_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2440k 100 2440k 0 0 10.9M 0 --:--:-- --:--:-- --:--:-- 11.1M
install for i386
* installing *source* package 'RTCGA' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RTCGA'
finding HTML links ... done
RTCGA-package html
boxplotTCGA html
finding level-2 HTML links ... done
checkTCGA html
convertTCGA html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:23: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/convertTCGA.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
datasetsTCGA html
downloadTCGA html
expressionsTCGA html
heatmapTCGA html
infoTCGA html
installTCGA html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpyKtFce/R.INSTALL1ec448d2566b/RTCGA/man/installTCGA.Rd:16: file link 'install_github' in package 'devtools' does not exist and so has been treated as a topic
kmTCGA html
mutationsTCGA html
pcaTCGA html
readTCGA html
survivalTCGA html
theme_RTCGA html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'RTCGA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA' as RTCGA_1.16.0.zip
* DONE (RTCGA)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'RTCGA' successfully unpacked and MD5 sums checked
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RTCGA.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(RTCGA)
Welcome to the RTCGA (version: 1.16.0).
> library(RTCGA.rnaseq)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
> #library(RTCGA.CNV)
> #library(RTCGA.PANCAN12)
>
> test_check("RTCGA")
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB
== testthat results ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
11.06 1.50 13.70
|
RTCGA.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(RTCGA)
Welcome to the RTCGA (version: 1.16.0).
> library(RTCGA.rnaseq)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
> #library(RTCGA.CNV)
> #library(RTCGA.PANCAN12)
>
> test_check("RTCGA")
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB
== testthat results ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
11.89 0.79 13.40
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RTCGA.Rcheck/examples_i386/RTCGA-Ex.timings
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RTCGA.Rcheck/examples_x64/RTCGA-Ex.timings
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